Effect of Organic Farming on Structural and Functional Diversity of Soil Microbiome: Benefits and Risks

  • Vijay Laxmi Shrivas
  • Upma Singh
  • L. Weisskopf
  • P. Hariprasad
  • Shilpi SharmaEmail author


The significance of microbial diversity in soil has been demonstrated since decades. Assorted variety of microorganisms in soil is fundamental to support soil health, as an extensive diversity of microorganisms is associated with essential soil functions. Several abiotic and biotic factors have been reported to affect the structural and functional diversity of soil microbes. This chapter centers around information related to the application of different biological amendments, and their influential role in shaping soil microbial community diversity, and health. Specifically, it focuses on the application of different organic fertilizers, and their influence on the diversity of microbial communities in arable soil, and upon the risks associated with such amendments, since they can be a source of heavy metals, antibiotics, antibiotic-resistant bacteria, and antibiotic-resistant genes carried by mobile genetic elements.


Organic farming Microbial diversity Animal manure Antibiotic resistance 



The study was supported by grants received from the Department of Biotechnology, Government of India (BT/PR27680/BCE/8/1434/2018), and Science and Engineering Research Board, Government of India (YSS/2015/001437). US wishes to acknowledge the fellowship received from the University Grant Commission, Government of India.


  1. Abdelfattah A, Wisniewski M, Droby S, Schena L (2016) Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase. Hort J 3:16047Google Scholar
  2. Ashworth AJ, DeBruyn JM, Allen FL, Radosevich M, Owens PR (2017) Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage. Soil Biol Biochem 114:210–219CrossRefGoogle Scholar
  3. Bailón-Salas AM, Medrano-Roldán H, Valle-Cervantes S, Ordaz-Díaz LA, Urtiz-Estrada N, Rojas-Contreras JA (2017) Review of molecular techniques for the identification of bacterial communities in biological effluent treatment facilities at pulp and paper mills. Bio Res 12:4384–4409Google Scholar
  4. Bashan Y, de-Bashan LE, Prabhu SR, Hernandez JP (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil 378:1–33CrossRefGoogle Scholar
  5. Beenhouwer MD, Van Geel M, Ceulemans T, Muleta D, Lievens B, Honnay O (2015) Changing soil characteristics alter the arbuscular mycorrhizal fungi communities of Arabica coffee (Coffea arabica) in Ethiopia across a management intensity gradient. Soil Biol Biochem 91:133–139CrossRefGoogle Scholar
  6. Bengtsson J, Ahnström J, Weibull AC (2005) The effects of organic agriculture on biodiversity and abundance: a meta-analysis. J Appl Ecol 42:261–269CrossRefGoogle Scholar
  7. Bhushan C, Khurana A, Sinha R, Nagaraju M (2017) Antibiotic resistance in poultry environment: spread of resistance from poultry farm to agricultural field. CSE:1–36Google Scholar
  8. Bian R, Joseph S, Cui L, Pan G, Li L, Liu X, Marjo C (2014) A three-year experiment confirms continuous immobilization of cadmium and lead in contaminated paddy field with biochar amendment. J Hazard Mater 272:121–128PubMedCrossRefGoogle Scholar
  9. Binh CTT, Heuer H, Kaupenjohann M, Smalla K (2008) Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol Ecol 66:25–37PubMedCrossRefGoogle Scholar
  10. Bonkowski M, Roy J (2005) Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms. Oecologia 143:232–240PubMedCrossRefGoogle Scholar
  11. Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities: effects of agricultural management season and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1–12PubMedCrossRefGoogle Scholar
  12. Brienen RJ, Phillips OL, Feldpausch TR, Gloor E, Baker TRL, Loyd J, Martinez RV (2015) Long-term decline of the Amazon carbon sink. Nature 519:344PubMedCrossRefGoogle Scholar
  13. Chen QL, An XL, Li H, Zhu YG, Su JQ, Cui L (2017) Do manure-borne or indigenous soil microorganisms influence the spread of antibiotic resistance genes in manured soil ? Soil Biol Biochem 114:229–237CrossRefGoogle Scholar
  14. Das S, Jeong ST, Das S, Kim PJ (2017) Composted cattle manure increases microbial activity and soil fertility more than composted swine manure in a submerged rice paddy. Front Microbol 8:1702CrossRefGoogle Scholar
  15. Dever LA, Dermody TS (1991) Mechanisms of bacterial resistance to antibiotics. Arch Intern Med 151:886–895PubMedCrossRefGoogle Scholar
  16. Ding LJ, Su JQ, Sun GX, Wu JS, Wei WX (2018) Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil. Appl Microbiol Biotechnol 102:1969–1982PubMedCrossRefGoogle Scholar
  17. Dumontet S, Cavoski I, Ricciuti P, Mondelli D, Jarrar M, Pasquale V, Crecchio C (2017) Metabolic and genetic patterns of soil microbial communities in response to different amendments under organic farming system. Geoderma 296:79–85CrossRefGoogle Scholar
  18. Enne VI, Cassar C, Sprigings K, Woodward MJ, Bennett PM (2008) A high prevalence of antimicrobial resistant Escherichia coli isolated from pigs and a low prevalence of antimicrobial resistant E. coli from cattle and sheep in Great Britain at slaughter. FEMS Microbiol Lett 278:193–199PubMedCrossRefGoogle Scholar
  19. Faldynova M, Videnska P, Havlickova H, Sisak F, Juricova H, Babak V, Steinhauser L, Rychlik I (2013) Prevalence of antibiotic resistance genes in faecal samples from cattle pigs and poultry. Vet Med - Czech 58:298–304CrossRefGoogle Scholar
  20. Fengsong Z, Yanxia LI, Ming Y, Wei LI, Weijin YAN (2011) Copper residue in animal manures and the potential pollution risk in northeast China. Mol Ecol Resour 2:91–96Google Scholar
  21. García-Orenes F, Guerrero C, Roldán A, Mataix-Solera J, Cerdà A, Campoy M, Caravaca F (2010) Soil microbial biomass and activity under different agricultural management systems in a semiarid Mediterranean agroecosystem. Soil Tillage Res 109:110–115CrossRefGoogle Scholar
  22. Halling-Sørensen B, Jacobsen AM, Jensen J, Sengeløv G, Vaclavik E, Ingerslev F (2005) Dissipation and effects of chlortetracycline and tylosin in two agricultural soils: a field-scale study in southern Denmark. Environ Toxicol Chem 24:802–810PubMedCrossRefPubMedCentralGoogle Scholar
  23. Hamscher G, Pawelzick HT, Höper H, Nau H (2005) Different behavior of tetracyclines and sulfonamides in sandy soils after repeated fertilization with liquid manure. Environ Toxicol Chem 24:861–868PubMedCrossRefPubMedCentralGoogle Scholar
  24. Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K (2018) Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 6:1–14CrossRefGoogle Scholar
  25. He Z, Endale DM, Schomberg HH, Jenkins MB (2009) Total phosphorus zinc copper and manganese concentrations in cecil soil through 10 years of poultry litter application. Soil Sci 174:687–695CrossRefGoogle Scholar
  26. Henneron L, Bernard L, Hedde M, Pelosi C, Villenave C, Chenu C, Blanchart E (2015) Fourteen years of evidence for positive effects of conservation agriculture and organic farming on soil life. Agron Sustain Dev 35:169–181CrossRefGoogle Scholar
  27. Hobbs PR, Sayre K, Gupta R (2008) The role of conservation agriculture in sustainable agriculture. Philos Trans R Soc Lond Ser B Biol Sci 363:543–555CrossRefGoogle Scholar
  28. Hu X, Zhou Q, Luo Y (2010) Occurrence and source analysis of typical veterinary antibiotics in manure, soil, vegetables and groundwater from organic vegetable bases, northern China. Enviro Pol 158:2992–2998CrossRefGoogle Scholar
  29. Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3:0003.1–0003.8CrossRefGoogle Scholar
  30. Johnston AE, Poulton PR, Coleman K (2009) Soil organic matter: its importance in sustainable agriculture and carbon dioxide fluxes. Adv Agron 101:1–57CrossRefGoogle Scholar
  31. Laird DA (2008) The charcoal vision: a win–win–win scenario for simultaneously producing bioenergy permanently sequestering carbon while improving soil and water quality. Agron J 100:178–181CrossRefGoogle Scholar
  32. Lazcano C, Gómez-Brandón M, Revilla P, Domínguez J (2013) Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function. Biol Fert Soils 49:723–733CrossRefGoogle Scholar
  33. Liu Y, Zhu J, Ye C, Zhu P, Ba Q, Pang J, Shu L (2018) Effects of biochar application on the abundance and community composition of denitrifying bacteria in a reclaimed soil from coal mining subsidence area. Sci Total Environ 625:1218–1224PubMedCrossRefPubMedCentralGoogle Scholar
  34. Lupatini M, Korthals GW, de Hollander M, Janssens TK, Kuramae EE (2017) Soil microbiome is more heterogeneous in organic than in conventional farming system. Front Microbiol 7:2064PubMedPubMedCentralCrossRefGoogle Scholar
  35. Lyngwi NA, Koijam K, Sharma D, Joshi SR (2013) Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya. Rev Biol Trop 61:467–490PubMedCrossRefPubMedCentralGoogle Scholar
  36. Mäder P, Fliessbach A, Dubois D, Gunst L, Fried P, Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296:1694–1697PubMedCrossRefPubMedCentralGoogle Scholar
  37. Marschner P, Kandeler E, Marschner B (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453–461CrossRefGoogle Scholar
  38. Marti R, Scott A, Tien YC, Murray R, Sabourin L, Zhang Y, Topp E (2013) The impact of manure fertilization on the abundance of antibiotic-resistant bacteria and frequency of detection of antibiotic resistance genes in soil, and on vegetables at harvest. Appl Environ Microbiol 79:5701–5709PubMedPubMedCentralCrossRefGoogle Scholar
  39. Mazzola M, Funnell DL, Raaijmakers JM (2004) Wheat cultivar-specific selection of 2 4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations. Microb Ecol 48:338–348PubMedCrossRefGoogle Scholar
  40. Mendes LW, Tsai SM, Navarrete AA, De Hollander M, van Veen JA, Kuramae EE (2015) Soil-borne microbiome: linking diversity to function. Microb Ecol 70:255–265CrossRefGoogle Scholar
  41. Nicholson PS, Hirsch PR (1998) The effects of pesticides on the diversity of culturable soil bacteria. J Appl Microbiol 84:551–558CrossRefGoogle Scholar
  42. Ollivier J, Schacht D, Kindler R, Groeneweg J, Engel M, Wilke BM, Kleineidam K, Schloter M (2013) Effects of repeated application of sulfadiazine-contaminated pig manure on the abundance and diversity of ammonia and nitrite oxidizers in the root-rhizosphere complex of pasture plants under field conditions. Front Microbiol 4:1–14CrossRefGoogle Scholar
  43. Pérez MT, Sommaruga R (2006) Differential effect of algal-and soil-derived dissolved organic matter on alpine lake bacterial community composition and activity. Limnol Oceanogr 51:2527–2537CrossRefGoogle Scholar
  44. Pornsukarom S, Thakur S (2017) Horizontal dissemination of antimicrobial resistance determinants in multiple Salmonella serotypes following isolation from the commercial swine operation environment after manure application. J Appl Environ Microbiol 83:1–14CrossRefGoogle Scholar
  45. Prosdocimi M, Jordán A, Tarolli P, Keesstra S, Novara A, Cerdà A (2016) The immediate effectiveness of barley straw mulch in reducing soil erodibility and surface runoff generation in Mediterranean vineyards. Sci Total Environ 547:323–330PubMedCrossRefGoogle Scholar
  46. Reganold JP, Wachter JM (2011) Agron 3610 | farming system and sustainable agriculture. Organic agriculture in the twenty-first century. Nat Plants 2:15221CrossRefGoogle Scholar
  47. Reichel R, Rosendahl I, Peeters ETHM, Focks A, Groeneweg J, Bierl R, Schlichting A, Amelung W, Thiele-Bruhn S (2013) Effects of slurry from sulfadiazine- (SDZ) and difloxacin- (DIF) medicated pigs on the structural diversity of microorganisms in bulk and rhizosphere soil. Soil Biol Biochem 62:82–91CrossRefGoogle Scholar
  48. Rondon MR, Goodman RM, Handelsman J (1999) The Earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17:403–409PubMedCrossRefGoogle Scholar
  49. Santamaría J, Parrado CA, López L (2017) Soil microbial community structure and diversity in cut flower cultures under conventional and ecological management. Rev Bras Ciênc Solo 42Google Scholar
  50. Schneider KD, Lynch DH, Dunfield K, Khosla K, Jansa J, Voroney RP (2015) Farm system management affects community structure of arbuscular mycorrhizal fungi. Appl Soil Ecol 96:192–200CrossRefGoogle Scholar
  51. Su JQ, Wei B, Xu CY, Qiao M, Zhu YG (2014) Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China. Environ Int 65:9–15PubMedCrossRefGoogle Scholar
  52. Tardy V, Spor A, Mathieu O, Leveque J, Terrat S, Plassart P, Régnier T, Bardgett RD, van der Putten W, Roggero PP, Seddaiu G, Bagella S, Lemanceau P, Ranjard L, Maron PA (2015) Shifts in microbial diversity through land use intensity as drivers of carbon mineralization in soil. Soil Biol Biochem 90:204–2013CrossRefGoogle Scholar
  53. TerAvest D, Carpenter-Boggs L, Thierfelder C, Reganold JP (2016) Crop production and soil water management in conservation agriculture no-till and conventional tillage systems in Malawi. Agric Ecosyst Environ 212:285–296CrossRefGoogle Scholar
  54. Tien YC, Li B, Zhang T, Scott A, Murray R, Sabourin L, Marti R, Topp E (2017) Impact of dairy manure pre-application treatment on manure composition soil dynamics of antibiotic resistance genes and abundance of antibiotic-resistance genes on vegetables at harvest. Sci Total Environ 581–582:32–39PubMedCrossRefGoogle Scholar
  55. Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J (2014) Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc Natl Acad Sci USA 111:15202–15207PubMedCrossRefGoogle Scholar
  56. Valentine DL, Kessler JD, Redmond MC, Mendes SD, Heintz MB, Farwell C, Chan EW (2010) Propane respiration jump-starts microbial response to a deep oil spill. Science 330:208–211PubMedCrossRefGoogle Scholar
  57. Velmourougane K (2016) Impact of organic and conventional systems of coffee farming on soil properties and culturable microbial diversity. Scientifica 2016:3604026–3604026PubMedPubMedCentralCrossRefGoogle Scholar
  58. Wang JJ, Li XY, Zhu AN, Zhang XK, Zhang HW, Liang WJ (2012) Effects of tillage and residue management on soil microbial communities in North China. Plant Soil Environ 58:28–33CrossRefGoogle Scholar
  59. Wang W, Wang H, Feng Y, Wang L, Xiao X, Xi Y, Luo X, Sun R, Ye X, Huang Y, Zhang Z (2016) Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze river. Sci Rep 6:35046PubMedPubMedCentralCrossRefGoogle Scholar
  60. Wardle DA (1995) Impacts of disturbance on detritus food webs in agro-ecosystems of contrasting tillage and weed management practices. Adv Ecol Res 26:105–185CrossRefGoogle Scholar
  61. Wardle DA, Yeates GW, Watson RN, Nicholson KS (1995) The detritus food-web and the diversity of soil fauna as indicators of disturbance regimes in agro-ecosystems. Plant Soil 170:35–43CrossRefGoogle Scholar
  62. Willer H, Lernoud J (eds) (2018) The world of organic agriculture. Statistics and emerging trends 2018. Research Institute of Organic Agriculture (FiBL), Frick, and IFOAM – Organics International, BonnGoogle Scholar
  63. Williams CM (2002) Nutritional quality of organic food: shades of grey or shades of green? Proc Nutr Soc 61:19–24PubMedCrossRefPubMedCentralGoogle Scholar
  64. Xiong W, Guo S, Jousset A, Zhao Q, Wu H, Li R, Shen Q (2017) Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome. Soil Biol Biochem 114:238–247CrossRefGoogle Scholar
  65. Xue K, Wu L, Deng Y, He Z, van Nostrand J, Robertson PG, Zhou J (2013) Functional gene differences in soil microbial communities from conventional low-input and organic farmlands. Appl Environ Microbiol 79:1284–1292PubMedPubMedCentralCrossRefGoogle Scholar
  66. Yeom JR, Yoon SU, Kim CG (2017) Quantification of residual antibiotics in cow manure being spread over agricultural land and assessment of their behavioral effects on antibiotic resistant bacteria. Chemosphere 182:771–780PubMedCrossRefPubMedCentralGoogle Scholar
  67. You F, Dalal R, Huang L (2018) Biochar and biomass organic amendments shaped different dominance of lithoautotrophs and organoheterotrophs in microbial communities colonizing neutral copper (Cu)-molybdenum (Mo)-gold (Au) tailings. Geoderma 309:100–110CrossRefGoogle Scholar
  68. Zhang F, Li Y, Yang M, Li W (2012) Content of heavy metals in animal feeds and manures from farms of different scales in Northeast China. Int J Environ Res Public Health 9:2658–2668PubMedPubMedCentralCrossRefGoogle Scholar
  69. Zhang Q, Wu J, Yang F, Lei Y, Zhang Q, Cheng X (2016) Alterations in soil microbial community composition and biomass following agricultural land use change. Sci Rep 6:36587PubMedPubMedCentralCrossRefGoogle Scholar
  70. Zhao L, Dong YH, Wang H (2010) Residues of veterinary antibiotics in manures from feedlot livestock in eight provinces of China. Sci Total Environ 408:1069–1075PubMedCrossRefPubMedCentralGoogle Scholar
  71. Zhen Z, Liu H, Wang N, Guo L, Meng J, Ding N, Wu G, Jiang G (2014) Effects of manure compost application on soil microbial community diversity and soil microenvironments in a temperate cropland in China. PLoS One 9:e108555PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Vijay Laxmi Shrivas
    • 1
    • 2
  • Upma Singh
    • 1
  • L. Weisskopf
    • 3
  • P. Hariprasad
    • 2
  • Shilpi Sharma
    • 1
    Email author
  1. 1.Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiHauz KhasIndia
  2. 2.Centre for Rural Development and TechnologyIndian Institute of Technology DelhiHauz KhasIndia
  3. 3.Department of BiologyUniversity of FribourgFribourgSwitzerland

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